Elevated levels of IRF1 and CASP1 as pyroptosis-related biomarkers for intestinal epithelial cells in Crohn's disease

Front Immunol. 2025 Feb 13:16:1551547. doi: 10.3389/fimmu.2025.1551547. eCollection 2025.

Abstract

Introduction: Crohn's disease (CD) is a complex inflammatory condition with the potential for severe complications. Pyroptosis is an inflammatory form of programmed cell death, and the role of pyroptosis in intestinal epithelial cells of CD remains unclear.

Methods: In this study, pyroptosis-related hub genes were identified using datasets from the Gene Expression Omnibus database through differential expression analysis, machine learning algorithms, and single-cell sequencing analysis. Hub gene expression was validated using clinical samples and a trinitrobenzene sulfonic acid (TNBS)-induced colitis rat model.

Results: Six pyroptosis-related hub genes (CASP1, IRF1, ZBP1, MLKL, MMP1, HTRA1) were identified. IRF1 and CASP1 exhibited significant upregulation in CD, including both colonic and ileal subtypes, with good diagnostic value across different CD subtypes. Additionally, these two genes were not elevated in any other intestinal disorders, except for ulcerative colitis. Single-cell sequencing analysis revealed a significant interaction between intestinal epithelial cells (IECs) and monocytes. The clinical samples further confirmed that the mRNA levels of IRF1 and CASP1 were significantly higher in CD patients compared to healthy controls. Additionally, the colitis rat model validated the upregulation of Irf1 and Casp1 at both mRNA and protein levels.

Conclusion: Our findings identified IRF1 and CASP1 as critical pyroptosis-related biomarkers for IECs in CD, contributing to the understanding of pyroptosis in CD pathogenesis.

Keywords: Crohn’s disease; biomarkers; bulk RNA sequencing; intestinal epithelial cells; pyroptosis; single-cell RNA sequencing.

MeSH terms

  • Animals
  • Biomarkers / metabolism
  • Caspase 1* / genetics
  • Caspase 1* / metabolism
  • Crohn Disease* / genetics
  • Crohn Disease* / metabolism
  • Crohn Disease* / pathology
  • Disease Models, Animal
  • Epithelial Cells* / metabolism
  • Epithelial Cells* / pathology
  • Female
  • Humans
  • Interferon Regulatory Factor-1* / genetics
  • Interferon Regulatory Factor-1* / metabolism
  • Intestinal Mucosa* / metabolism
  • Intestinal Mucosa* / pathology
  • Male
  • Pyroptosis* / genetics
  • Rats

Substances

  • Interferon Regulatory Factor-1
  • Caspase 1
  • Biomarkers
  • IRF1 protein, human

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by the National Natural Science Foundation of China (grant number 81860104); the Natural Science Foundation of Guangxi Zhuang Autonomous Region (grant number 2017GXNSFAA198299); the Development and Application of Medical and Health Appropriate Technology Project in Guangxi Zhuang Autonomous Region (grant number S2018049); the Self-financing Project of Health Commission of Guangxi Zhuang Autonomous Region (grant number Z20200398); the Self-financing Project of Health Commission of Guangxi Zhuang Autonomous Region (grant number Z-A20230474); the Youth Science Foundation of Guangxi Medical University (grant number GXMUYSF202316).